[gentoo-commits] proj/sci:master commit in: sci-biology/blue/

[gentoo-commits] proj/sci:master commit in: sci-biology/blue/

[Martin Mokrejs]

commit:     0322af051993bb9cfbcf22a9e544bc01b18a54a0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 13:55:55 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 13:55:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0322af05

sci-biology/blue: version bump, updated HOMEPAGE and SRC_URI

Package-Manager: portage-2.2.18

 sci-biology/blue/ChangeLog         |  6 ++++++
 sci-biology/blue/blue-1.1.2.ebuild | 12 ++++++++----
 sci-biology/blue/blue-1.1.3.ebuild | 38 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
index cbcd718..97f6844 100644
--- a/sci-biology/blue/ChangeLog
+++ b/sci-biology/blue/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*blue-1.1.3 (26 May 2015)
+
+  26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.3.ebuild,
+  blue-1.1.2.ebuild:
+  sci-biology/blue: version bump, updated HOMEPAGE and SRC_URI
+
   17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> blue-1.1.2.ebuild:
   improved comments based on email from upstream
 

diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
index 5b9ed96..945a35d 100644
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -5,11 +5,11 @@
 EAPI=5
 
 DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
-HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx"
+HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
 SRC_URI="
-	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> ${P}.tar.gz
-	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf"
-
+	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
+	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
+	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
 LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS=""
@@ -29,6 +29,10 @@ src_compile(){
 src_install(){
 	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
 	# one could install also the *.exe.so files for speedup into /usr/bin/
+
+	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. 
+
+	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
 }
 
 # it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector

diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild
new file mode 100644
index 0000000..945a35d
--- /dev/null
+++ b/sci-biology/blue/blue-1.1.3.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
+HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
+SRC_URI="
+	http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
+	http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf
+	http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf"
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/mono"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/Linux
+
+src_compile(){
+	Blue/compile.sh || die
+	Tessel/compile.sh || die
+	GenerateMerPairs/compile.sh || die
+}
+
+src_install(){
+	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
+	# one could install also the *.exe.so files for speedup into /usr/bin/
+
+	# The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. 
+
+	# In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently?
+}
+
+# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector

[gentoo-commits] proj/sci:master commit in: sci-biology/blue/

[Martin Mokrejs]

commit:     30607dc2f8976d7f1930a677c676ae01c95cea30
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 14:23:41 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 14:23:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=30607dc2

improved comments based on email from upstream

Package-Manager: portage-2.2.15

 sci-biology/blue/ChangeLog         | 4 +++-
 sci-biology/blue/blue-1.1.2.ebuild | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
index 9dcc134..cbcd718 100644
--- a/sci-biology/blue/ChangeLog
+++ b/sci-biology/blue/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> blue-1.1.2.ebuild:
+  improved comments based on email from upstream
+
   10 Jan 2015; Justin Lecher <jlec@gentoo.org> blue-1.1.2.ebuild:
   Fix license
 
@@ -10,4 +13,3 @@
   07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild,
   +metadata.xml:
   Initial ebuild, does not install the *.exe.so files. Do we need them?
-

diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
index 834db7c..5b9ed96 100644
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -28,5 +28,7 @@ src_compile(){
 
 src_install(){
 	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
-	# BUG: probably have to install also the *.exe.so files
+	# one could install also the *.exe.so files for speedup into /usr/bin/
 }
+
+# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector

[gentoo-commits] proj/sci:master commit in: sci-biology/blue/

[Justin Lecher]

commit:     3f6a27b07fb75fe134e05e7487f301f02fbb77a6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:38:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:38:06 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f6a27b0

sci-biology/blue: Fix license

Package-Manager: portage-2.2.15

---
 sci-biology/blue/ChangeLog         | 3 +++
 sci-biology/blue/blue-1.1.2.ebuild | 5 +++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
index 7c74563..9dcc134 100644
--- a/sci-biology/blue/ChangeLog
+++ b/sci-biology/blue/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Justin Lecher <jlec@gentoo.org> blue-1.1.2.ebuild:
+  Fix license
+
 *blue-1.1.2 (07 Jan 2015)
 
   07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild,

diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
index a4555b3..834db7c 100644
--- a/sci-biology/blue/blue-1.1.2.ebuild
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -6,10 +6,11 @@ EAPI=5
 
 DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
 HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx"
-SRC_URI="http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> "${P}".tar.gz
+SRC_URI="
+	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> ${P}.tar.gz
 	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf"
 
-LICENSE="GPL"
+LICENSE="GPL-2+"
 SLOT="0"
 KEYWORDS=""
 IUSE=""

[gentoo-commits] proj/sci:master commit in: sci-biology/blue/

[Martin Mokrejs]

commit:     461b242fee3a125f00e7de8fedbf7e20b3392683
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan  7 22:00:08 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan  7 22:00:08 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=461b242f

Initial ebuild, does not install the *.exe.so files. Do we need them?

---
 sci-biology/blue/ChangeLog         | 10 ++++++++++
 sci-biology/blue/blue-1.1.2.ebuild | 31 +++++++++++++++++++++++++++++++
 sci-biology/blue/metadata.xml      |  9 +++++++++
 3 files changed, 50 insertions(+)

diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog
new file mode 100644
index 0000000..7c74563
--- /dev/null
+++ b/sci-biology/blue/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/blue
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*blue-1.1.2 (07 Jan 2015)
+
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild,
+  +metadata.xml:
+  Initial ebuild, does not install the *.exe.so files. Do we need them?
+

diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
new file mode 100644
index 0000000..a4555b3
--- /dev/null
+++ b/sci-biology/blue/blue-1.1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
+HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx"
+SRC_URI="http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> "${P}".tar.gz
+	http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf"
+
+LICENSE="GPL"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/mono"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/Linux
+
+src_compile(){
+	Blue/compile.sh || die
+	Tessel/compile.sh || die
+	GenerateMerPairs/compile.sh || die
+}
+
+src_install(){
+	dobin Tessel.exe GenerateMerPairs.exe Blue.exe
+	# BUG: probably have to install also the *.exe.so files
+}

diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/blue/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>